Core 2: Software Infrastructure for Network Models and Cell Maps

CCMI v2.0 核心2：用于网络模型和单元图的软件基础设施 核心负责人：Trey Ideker；联合调查员：Dexter Pratt 摘要 网络模型和单元地图核心的软件基础设施将完全支持CCMI项目 研究和出版的各个阶段。核心将向以下三个主要方面提供基础设施和援助 要素：(1)Cytoscape桌面应用程序以及来自Cytoscape生态系统的工具和服务； (2)NDEX，即网络数据交换；和(3)开发和部署Web的基础设施 服务和应用程序。首先，我们将支持中心调查人员使用细胞景观生态系统来 生物网络的分析和可视化，包括项目1中的蛋白质-蛋白质相互作用网络， 来自项目2的遗传相互作用网络，以及来自项目3的多尺度癌细胞图。 生态系统包括著名的Cytoscape桌面环境、HiView多比例细胞模型查看器、 IQuery途径分析工具、多个R和Python库，以及用于 多尺度细胞模型的生成。第二，我们将促进中心调查人员使用NDeX发布 CCMI单元图、交互数据和其他产品作为可立即可视化的“实时”网络数据 并被利用。我们还将在使用NDX共享出版前网络数据方面提供帮助 中心调查人员，包括从Jupyter笔记本电脑和其他软件直接、编程访问。第三, 我们将在创建网络界面和后端服务方面向项目3调查人员提供协助。 对于所有项目，我们将促进以编程方式访问资源、托管网站、使用Docker 软件容器和CCMI Github存储库的管理。最后，我们将维护和扩展 CCMI网络门户，通过NDeX网络云提供对(1)CCMI公共网络和小区地图的访问，(2) CCMI软件工具和资源，(3)定制网站和Web应用程序CCMI v2.0

CCMI v2.0 Core 2: Software Infrastructure for Network Models and Cell Maps Core Lead: Trey Ideker; Co-Investigator: Dexter Pratt SUMMARY The Software Infrastructure for Network Models and Cell Maps Core will support the CCMI Projects at all stages of research and publication. The core will provide infrastructure and assistance towards three main elements: (1) the Cytoscape desktop application along with tools and services from the Cytoscape Ecosystem; (2) NDEx, the Network Data Exchange; and (3) infrastructure for the development and deployment of web services and applications. First, we will support center investigators in use of the Cytoscape Ecosystem for analysis and visualization of biological networks, including protein--protein interaction networks from Project 1, genetic interaction networks from Project 2, and multiscale cancer cell maps from Project 3. The Cytoscape Ecosystem includes the well-known Cytoscape desktop environment, the HiView multiscale cell model viewer, the IQuery pathway analysis tool, multiple R and Python libraries, and the CDAPS software framework for the generation of multiscale cell models. Second, we will facilitate the use of NDEx by center investigators to publish CCMI cell maps, interaction data, and other products as “live” network data that can be immediately visualized and used. We will also provide assistance in the use of NDEx to share pre-publication network data between center investigators, including direct, programmatic access from Jupyter notebooks and other software. Third, we will provide assistance to Project 3 investigators in the creation of web interfaces and back-end services. For all projects, we will facilitate programmatic access to resources, hosting of websites, the use of Docker software containers, and the management of CCMI Github repositories. Finally, we will maintain and extend the CCMI web portal to provide access to (1) CCMI public networks and cell maps via the NDEx networks cloud, (2) CCMI software tools and resources, (3) custom websites and web applications CCMI v2.0